The focal length of pretty much every lens changes depending on focusing distance, so once you focus close with e.g. a 50mm lens, it is most likely not exactly 50mm anymore, so the DOF calculator is a little tricky to use. How much it changes depends on lens, so I don't think any calculator compensates for it.

Nor does a "50mm" lens necessarily have a focal length of exactly 50mm at any distance. The focal length designations for lenses are like "two litre" engines: they are rarely exactly that. To give one example of both issues, the Nikon 70-200 f/2.8 VRII is, in fact, 72-192mm at infinity, and at close focus is 70-134mm!